Your question is far, far too general.
There could be potential holes in the SQL code, which could let in SQL injection exploits.
There could be ways for hackers to finagle the PHP code, if the programmer(s) didn't write it cleanly and securely.
There could be exploitable flaws in the Perl scripts used, in the PHP in the pages themselves, in the JavaScript...the list goes on.
If you want answers, you'll need to narrow your question quite a bit.
Your best bet to learn this stuff is to hang around websites and communities whose main theme is web programming and development - specifically, those languages which you intend to use.
